     (cond
       (:help options) (exit 0 (usage summary))
       errors (exit 1 (error-msg errors)))
-    (config-logging (:log options))
+    (init-logging (:log options))
     (process-fasta-files (:minlen options) arguments)))

                   (bs/biosequence-seq reader)))))

(defn process-fasta-file
  [minlen filename]
  (timbre/info "Processing FASTA file from" filename)
  (with-open [reader (bs/bs-reader (bs/init-fasta-file filename :iupacAminoAcids))]
    (process-fasta-reader minlen filename reader)))

(defn process-stdin
  [minlen]
  (timbre/info "Processing FASTA file from stdin")
  (with-open [reader (bs/init-fasta-reader (java.io.BufferedReader. *in*) :iupacAminoAcids)]
    (process-fasta-reader minlen "stdin" reader)))

(def header "FILENAME\tTOTAL\tNUMSEQ\tMIN\tAVG\tMAX")

(defn process-fasta-files
  [minlen files]
  (println header)
  (if (empty? files)
    (process-stdin minlen)
    (doseq [file files]
      (process-fasta-file minlen file))))

(defn usage [options-summary]
  (->> ["Print fasta stats"
        ""
        "Usage: program-name [options] FILES"


;;; The main parts of the program are:
;;; 1. Parse command line arguments. 
;;; 2. Process each FASTA file in sequence.
;;; 3. Pretty print output for each file. 
;;;
;;; If no FASTA filenames are specified on the command line then the program
